[2023-06-16 20:50:18,354] [INFO] DFAST_QC pipeline started.
[2023-06-16 20:50:18,367] [INFO] DFAST_QC version: 0.5.7
[2023-06-16 20:50:18,367] [INFO] DQC Reference Directory: /var/lib/cwl/stg5ef91db7-58b9-4554-99e4-c1e77f80fca4/dqc_reference
[2023-06-16 20:50:19,689] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-16 20:50:19,690] [INFO] Task started: Prodigal
[2023-06-16 20:50:19,690] [INFO] Running command: gunzip -c /var/lib/cwl/stg7f5be068-3dba-441a-b465-0d7d3ea749bf/GCA_028293685.1_ASM2829368v1_genomic.fna.gz | prodigal -d GCA_028293685.1_ASM2829368v1_genomic.fna/cds.fna -a GCA_028293685.1_ASM2829368v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-16 20:50:25,439] [INFO] Task succeeded: Prodigal
[2023-06-16 20:50:25,439] [INFO] Task started: HMMsearch
[2023-06-16 20:50:25,439] [INFO] Running command: hmmsearch --tblout GCA_028293685.1_ASM2829368v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5ef91db7-58b9-4554-99e4-c1e77f80fca4/dqc_reference/reference_markers.hmm GCA_028293685.1_ASM2829368v1_genomic.fna/protein.faa > /dev/null
[2023-06-16 20:50:25,615] [INFO] Task succeeded: HMMsearch
[2023-06-16 20:50:25,616] [INFO] Found 6/6 markers.
[2023-06-16 20:50:25,640] [INFO] Query marker FASTA was written to GCA_028293685.1_ASM2829368v1_genomic.fna/markers.fasta
[2023-06-16 20:50:25,640] [INFO] Task started: Blastn
[2023-06-16 20:50:25,641] [INFO] Running command: blastn -query GCA_028293685.1_ASM2829368v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5ef91db7-58b9-4554-99e4-c1e77f80fca4/dqc_reference/reference_markers.fasta -out GCA_028293685.1_ASM2829368v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 20:50:26,426] [INFO] Task succeeded: Blastn
[2023-06-16 20:50:26,431] [INFO] Selected 23 target genomes.
[2023-06-16 20:50:26,431] [INFO] Target genome list was writen to GCA_028293685.1_ASM2829368v1_genomic.fna/target_genomes.txt
[2023-06-16 20:50:26,435] [INFO] Task started: fastANI
[2023-06-16 20:50:26,435] [INFO] Running command: fastANI --query /var/lib/cwl/stg7f5be068-3dba-441a-b465-0d7d3ea749bf/GCA_028293685.1_ASM2829368v1_genomic.fna.gz --refList GCA_028293685.1_ASM2829368v1_genomic.fna/target_genomes.txt --output GCA_028293685.1_ASM2829368v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-16 20:50:39,063] [INFO] Task succeeded: fastANI
[2023-06-16 20:50:39,063] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5ef91db7-58b9-4554-99e4-c1e77f80fca4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-16 20:50:39,064] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5ef91db7-58b9-4554-99e4-c1e77f80fca4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-16 20:50:39,081] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2023-06-16 20:50:39,082] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-16 20:50:39,082] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Lysobacter profundi	strain=CHu50b-3-2	GCA_009792795.1	2594501	2594501	type	True	81.436	398	549	95	below_threshold
Luteimonas weifangensis	strain=WF-2	GCA_003416885.1	2303539	2303539	type	True	79.7322	305	549	95	below_threshold
Luteimonas cucumeris	strain=CGMCC 1.10821	GCA_007830035.1	985012	985012	type	True	79.5593	272	549	95	below_threshold
Luteimonas mephitis	strain=DSM 12574	GCA_000422305.1	83615	83615	type	True	79.4096	263	549	95	below_threshold
Luteimonas aquatica	strain=RIB1-20	GCA_022662575.1	450364	450364	type	True	79.1392	267	549	95	below_threshold
Luteimonas lumbrici	strain=1.1416	GCA_006476065.1	2559601	2559601	type	True	79.134	250	549	95	below_threshold
Luteimonas terricola	strain=BZ92r	GCA_004352845.1	645597	645597	type	True	79.0973	215	549	95	below_threshold
Luteimonas marina	strain=FR1330	GCA_007859325.1	488485	488485	type	True	78.9371	261	549	95	below_threshold
Lysobacter dokdonensis	strain=DS-58	GCA_000770795.1	414050	414050	type	True	78.8748	235	549	95	below_threshold
Luteimonas panaciterrae	strain=Gsoil 068	GCA_020511115.1	363885	363885	type	True	78.8662	237	549	95	below_threshold
Lysobacter gilvus	strain=HX-5-24	GCA_009740395.1	2682097	2682097	type	True	78.8112	238	549	95	below_threshold
Lysobacter arseniciresistens	strain=ZS79	GCA_000768335.1	1385522	1385522	type	True	78.774	229	549	95	below_threshold
Vulcaniibacterium thermophilum	strain=KCTC 32020	GCA_014656335.1	1169913	1169913	type	True	78.7423	238	549	95	below_threshold
Vulcaniibacterium thermophilum	strain=KCTC 32020	GCA_007923255.1	1169913	1169913	type	True	78.7363	238	549	95	below_threshold
Luteimonas colneyensis	strain=Sa2BVA3	GCA_014836665.1	2762230	2762230	type	True	78.732	224	549	95	below_threshold
Luteimonas gilva	strain=H23	GCA_005239095.1	2572684	2572684	type	True	78.7266	263	549	95	below_threshold
Luteimonas arsenica	strain=26-35	GCA_004352825.1	1586242	1586242	type	True	78.7196	224	549	95	below_threshold
Luteimonas padinae	strain=KCTC 52403	GCA_014652935.1	1714359	1714359	type	True	78.7082	229	549	95	below_threshold
Luteimonas saliphila	strain=SJ-9	GCA_016774335.1	2804919	2804919	type	True	78.6941	251	549	95	below_threshold
Luteimonas viscosa	strain=XBU10	GCA_008244685.1	1132694	1132694	type	True	78.6776	249	549	95	below_threshold
Lysobacter soli	strain=KCTC 22011	GCA_003382285.1	453783	453783	type	True	78.6726	255	549	95	below_threshold
Lysobacter psychrotolerans	strain=ZS60	GCA_003719825.1	1327343	1327343	type	True	78.4741	241	549	95	below_threshold
Luteimonas salinisoli	strain=SJ-92	GCA_013425525.1	2752307	2752307	type	True	78.4702	247	549	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-16 20:50:39,084] [INFO] DFAST Taxonomy check result was written to GCA_028293685.1_ASM2829368v1_genomic.fna/tc_result.tsv
[2023-06-16 20:50:39,084] [INFO] ===== Taxonomy check completed =====
[2023-06-16 20:50:39,084] [INFO] ===== Start completeness check using CheckM =====
[2023-06-16 20:50:39,085] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5ef91db7-58b9-4554-99e4-c1e77f80fca4/dqc_reference/checkm_data
[2023-06-16 20:50:39,086] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-16 20:50:39,110] [INFO] Task started: CheckM
[2023-06-16 20:50:39,111] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_028293685.1_ASM2829368v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_028293685.1_ASM2829368v1_genomic.fna/checkm_input GCA_028293685.1_ASM2829368v1_genomic.fna/checkm_result
[2023-06-16 20:51:01,940] [INFO] Task succeeded: CheckM
[2023-06-16 20:51:01,941] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.79%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-16 20:51:01,960] [INFO] ===== Completeness check finished =====
[2023-06-16 20:51:01,960] [INFO] ===== Start GTDB Search =====
[2023-06-16 20:51:01,960] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_028293685.1_ASM2829368v1_genomic.fna/markers.fasta)
[2023-06-16 20:51:01,960] [INFO] Task started: Blastn
[2023-06-16 20:51:01,960] [INFO] Running command: blastn -query GCA_028293685.1_ASM2829368v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5ef91db7-58b9-4554-99e4-c1e77f80fca4/dqc_reference/reference_markers_gtdb.fasta -out GCA_028293685.1_ASM2829368v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 20:51:03,328] [INFO] Task succeeded: Blastn
[2023-06-16 20:51:03,332] [INFO] Selected 20 target genomes.
[2023-06-16 20:51:03,332] [INFO] Target genome list was writen to GCA_028293685.1_ASM2829368v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-16 20:51:03,401] [INFO] Task started: fastANI
[2023-06-16 20:51:03,401] [INFO] Running command: fastANI --query /var/lib/cwl/stg7f5be068-3dba-441a-b465-0d7d3ea749bf/GCA_028293685.1_ASM2829368v1_genomic.fna.gz --refList GCA_028293685.1_ASM2829368v1_genomic.fna/target_genomes_gtdb.txt --output GCA_028293685.1_ASM2829368v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-16 20:51:14,088] [INFO] Task succeeded: fastANI
[2023-06-16 20:51:14,105] [INFO] Found 20 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-16 20:51:14,105] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_009792795.1	s__Luteimonas_B profundi	81.4149	399	549	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011320095.1	s__Luteimonas_B telluris	80.7207	359	549	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003416885.1	s__Luteimonas_B sp003416885	79.715	306	549	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007830035.1	s__Luteimonas_C cucumeris	79.5407	273	549	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas_C	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013362405.1	s__JABFWF01 sp013362405	79.478	258	549	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__JABFWF01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000422305.1	s__Luteimonas mephitis	79.4096	263	549	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003586305.1	s__Lysobacter tabacisoli	79.2364	277	549	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006476065.1	s__Luteimonas_B lumbrici	79.134	250	549	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004352845.1	s__Luteimonas terricola	79.0753	216	549	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	99.99	99.99	0.99	0.99	2	-
GCA_004297225.1	s__Luteimonas_B sp004297225	78.9433	223	549	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014380115.1	s__JACMKK01 sp014380115	78.9383	242	549	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__JACMKK01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018406645.1	s__Lysobacter_A helvus	78.9374	262	549	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_007859325.1	s__Luteimonas marina	78.9285	262	549	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902825775.1	s__Luteimonas_C sp902825775	78.859	255	549	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017308985.1	s__Lysobacter sp017308985	78.8181	253	549	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007923255.1	s__Lysobacter thermophilus	78.7553	237	549	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	99.99	99.99	0.98	0.98	2	-
GCF_005239095.1	s__Luteimonas_C gilva	78.7428	262	549	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003719825.1	s__Lysobacter psychrotolerans	78.49	240	549	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017302135.1	s__SCMT01 sp017302135	78.1666	203	549	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__SCMT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013141175.1	s__SCMT01 sp013141175	78.0405	215	549	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__SCMT01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-16 20:51:14,107] [INFO] GTDB search result was written to GCA_028293685.1_ASM2829368v1_genomic.fna/result_gtdb.tsv
[2023-06-16 20:51:14,108] [INFO] ===== GTDB Search completed =====
[2023-06-16 20:51:14,113] [INFO] DFAST_QC result json was written to GCA_028293685.1_ASM2829368v1_genomic.fna/dqc_result.json
[2023-06-16 20:51:14,113] [INFO] DFAST_QC completed!
[2023-06-16 20:51:14,114] [INFO] Total running time: 0h0m56s